I am having an issue identifying primary objects (nuclei) using cell profiler. When do not use “advanced settings”, the segmentation is working semi correctly. See image below. One issue is that cell profiler is taking one nuclei and segmenting it into two. I’d like to use the “advanced settings” to edit the smoothing scale and the declumping options in order to remedy this issue.
However, when I do click on the use “advanced options”, cell profiler more or less completely fails to segment nuclei correctly. Rather is returning segmentation on the cell nuclei and then an additional bit of area which should be easily recognized as background. See image below.
Attached is my pipeline as well.
Nuclei Analysis.cpproj (653.8 KB)
Any help would be greatly appreciated